Special Issue "Insights into Antisense Long Non-Coding RNAs Metabolism and Expression"

A special issue of Non-Coding RNA (ISSN 2311-553X).

Deadline for manuscript submissions: 30 September 2022 | Viewed by 4736

Special Issue Editors

Dr. Maxime Wery
E-Mail Website
Guest Editor
ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR 3244, Paris, France
Interests: long non-coding RNA; antisense transcription; gene expression; post-transcriptional RNA metabolism; Nonsense-Mediated mRNA Decay; lncRNA-derived micropeptide; functional genomics
Dr. Julien Soudet
E-Mail Website
Guest Editor
Department of Cell Biology, University of Geneva, 1211 Geneva, Switzerland
Interests: non-coding transcription; antisense transcription; chromatin; gene regulation; nucleosomes; nucleosome-depleted regions

Special Issue Information

Dear Colleagues,

While initially considered as pervasive transcripts devoid of any regulatory function, long non-coding (lnc)RNAs have progressively emerged as key players involved in multiple cellular processes.

Among the different classes of lncRNAs, “antisense” (as)lncRNAs are synthesized from the DNA strand opposite to “sense” genes. Over the last few years, they have attracted a lot of attention given their potential to regulate gene expression.

Despite their regulatory importance, aslncRNAs still remain poorly characterized. One reason for this lack of global information on aslncRNAs appears to be their low cellular abundance. In fact, pioneering studies in yeast have highlighted the role of evolutionarily conserved RNA decay machineries in tightly controlling aslncRNAs levels.

In this context, this Special Issue will focus on the expression and the metabolism of aslncRNAs, including antisense transcription, the regulation of aslncRNAs expression and decay, the interactions of aslncRNAs with RNA/DNA, aslncRNAs as regulators of gene expression and other processes, aslncRNAs expression in cancer and diseases, and evolutionary aspects of aslncRNAs.

Manuscripts reporting original research, short communications, methods, and reviews will be considered.

Dr. Maxime Wery
Dr. Julien Soudet
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Non-Coding RNA is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Antisense transcription
  • aslncRNAs expression and decay
  • aslncRNAs metabolism
  • Regulatory aslncRNAs
  • aslncRNAs in cancer and disease

Published Papers (2 papers)

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Research

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Article
Interdependent Transcription of a Natural Sense/Antisense Transcripts Pair (SLC34A1/PFN3)
Non-Coding RNA 2022, 8(1), 19; https://doi.org/10.3390/ncrna8010019 - 11 Feb 2022
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Abstract
Natural antisense transcripts (NATs) constitute a significant group of regulatory, long noncoding RNAs. They are prominently expressed in testis but are also detectable in other organs. NATs are transcribed at low levels and co-expressed with related protein coding sense transcripts. Nowadays NATs are [...] Read more.
Natural antisense transcripts (NATs) constitute a significant group of regulatory, long noncoding RNAs. They are prominently expressed in testis but are also detectable in other organs. NATs are transcribed at low levels and co-expressed with related protein coding sense transcripts. Nowadays NATs are generally considered as regulatory, long noncoding RNAs without closer focus on the inevitable interference between sense and antisense expression. This work describes a cellular system where sense and antisense transcription of a specific locus (SLC34A1/PFN3) is induced using epigenetic modifiers and CRISPR-Cas9. The renal cell lines HEK293 and HKC-8 do not express SLC34A1/PFN3 under normal culture conditions. Five-day exposure to dexamethasone significantly stimulates sense transcript (SLC34A1) levels and antisense (PFN3) minimally; the effect is only seen in HEK293 cells. Enhanced expression is paralleled by reduced sense promoter methylation and an increase in activating histone marks. Expression is further modulated by cassettes that stimulate the expression of sense or antisense transcript but disrupt protein coding potential. Constitutive expression of a 5′-truncated SLC34A1 transcript increases sense expression independent of dexamethasone induction but also stimulates antisense expression. Concordant expression is confirmed with the antisense knock-in that also enhances sense expression. The antisense effect acts on transcription in cis since transient transfection with sense or antisense constructs fails to stimulate the expression of the opposite transcript. These results suggest that bi-directional transcription of the SLC34A1/PFN3 locus has a stimulatory influence on the expression of the opposite transcript involving epigenetic changes of the promoters. In perspective of extensive, previous research into bi-directionally transcribed SLC34A loci, the findings underpin a hypothesis where NATs display different biological roles in soma and germ cells. Accordingly, we propose that in somatic cells, NATs act like lncRNAs–with the benefit of close proximity to a potential target gene. In germ cells, however, recent evidence suggests different biological roles for NATs that require RNA complementarity and double-stranded RNA formation. Full article
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Review

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Review
From Yeast to Mammals, the Nonsense-Mediated mRNA Decay as a Master Regulator of Long Non-Coding RNAs Functional Trajectory
Non-Coding RNA 2021, 7(3), 44; https://doi.org/10.3390/ncrna7030044 - 27 Jul 2021
Cited by 5 | Viewed by 2525
Abstract
The Nonsense-Mediated mRNA Decay (NMD) has been classically viewed as a translation-dependent RNA surveillance pathway degrading aberrant mRNAs containing premature stop codons. However, it is now clear that mRNA quality control represents only one face of the multiple functions of NMD. Indeed, NMD [...] Read more.
The Nonsense-Mediated mRNA Decay (NMD) has been classically viewed as a translation-dependent RNA surveillance pathway degrading aberrant mRNAs containing premature stop codons. However, it is now clear that mRNA quality control represents only one face of the multiple functions of NMD. Indeed, NMD also regulates the physiological expression of normal mRNAs, and more surprisingly, of long non-coding (lnc)RNAs. Here, we review the different mechanisms of NMD activation in yeast and mammals, and we discuss the molecular bases of the NMD sensitivity of lncRNAs, considering the functional roles of NMD and of translation in the metabolism of these transcripts. In this regard, we describe several examples of functional micropeptides produced from lncRNAs. We propose that translation and NMD provide potent means to regulate the expression of lncRNAs, which might be critical for the cell to respond to environmental changes. Full article
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Antisense long non-coding RNAs located next to transcription factors and their roles in participation in transcriptional regulation
Authors: Yifan Bao; Anagha Gogate; Rajvi Parikh; Shiv Patel; Ross Bernstein; Xiao-bo Zhong
Affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA

Title: The Human Long Noncoding RNA Wilms Tumour 1 Antisense RNA Locus, from an Evolutionary Perspective to Functional Insights
Authors: Thuluz Meza-Menchaca; et al.
Affiliation: Laboratorio de Genómica Humana, Facultad de Medicina, Universidad Veracruzana, Médicos y Odontólogos S/N, Col. Unidad del Bosque, C.P. 91010 Xalapa, Veracruz, Mexico

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